Zeid Ra`ad Al Hussein said migrants had been strip-searched to find money to pay for their detention, and protested about "Islamophobic" statements by Czech President Milos Zeman.
The president`s spokesman said he `stood by his opinions`.
While other European countries had implemented policies to restrict the movement of migrants, the Czech Republic was "unique" in its routine detention of migrants for long periods, Mr Hussein said.
He said the measures taken appeared to be "designed to deter migrants and refugees from entering the country or staying there".
Mr Hussein said one detention facility in Beza-Jezova has been described as "worse than a prison" by the Czech justice minister.
Czechs accused of abusing migrants
22 October 2015
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The Czech Republic was holding migrants in "degrading" conditions for up to 90 days, the UN human rights chief said.
